4,444 Works

Supporting data and materials for \"Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat\"

Nicholas C Wong, Bernard J Pope, Ida Candiloro, Darren Korbie, Matt Trau, Stephen Q Wong, Thomas Mikeska, Bryce J Van Denderen, Erik W Thompson, Stefanie Eggers, Stephen Doyle & Alexander Dobrovic
DNA methylation is a complex epigenetic marker that can be analysed using a wide variety of methods. Interpretation and visualisation of DNA methylation data can mask complexity in terms of methylation status at each CpG site, cellular heterogeneity of samples and allelic DNA methylation patterns within a given DNA strand. Bisulfite sequencing is considered the gold standard, however visualisation of massively parallel sequencing results remains a significant challenge. We created a program called Methpat that...

The genome of the Australian dragon lizard Pogona vitticeps

Arthur Georges, , , Denis OMeally, Janine Deakin, , Pei Zhang, Matthew Fujita, Hardip R Patel, Clare E Holleley, Yang Zhou, , Kazumi Matsubara, Paul Waters, Jennifer AM Graves, Stephen D Sarre &
We present a genomic resource for a wild-caught male ZZ Central Bearded Dragon Pogona vitticeps, from Australia. The genomic sequence, generated on the Illumina HiSeq 2000 platform, comprised 317 Gbp (185x raw read depth) from 13 insert libraries ranging from 250 bp to 40 Kbp. After filtering for low quality and duplicated reads, a total of 146 Gbp of data (86x) was available for assembly. Exceptionally high levels of heterozygosity (0.85 % SNP plus indels)...

Supporting data for \"Evaluating a multigene environmental DNAapproach for comprehensive biodiversityassessment\"

Alexei J Drummond, Richard D Newcomb, Thomas R Buckley, Dong Xie, Andrew Dopheide, Benjamin CM Potter, Joseph Heled, Howard A Ross, Leah Tooman, Stefanie Grosser, , Nicholas J Demetras, Mark I Stevens, James C Russell, Sandra H Anderson, Anna Carter & Nicola Nelson
There is increasing demand for rapid biodiversity assessment tools that have broad taxonomic coverage. Traditional approaches typically rely on specialists for identification and only evaluate small subsets of biodiversity. Environmental DNA (eDNA) approaches are being promoted as a solution to these limitations, but questions remain unresolved. Here we evaluate a suite of DNA markers coupled with next generation sequencing (NGS) that span the tree of life. We compare these data to traditional biodiversity monitoring tools,...

Supporting data for the \"Draft genome of the Chinese mitten crab, Eriocheir sinensis\"

, Chao Bian, , , , Jia Li, Ying Qiu, , , Liang Ma, , Ying Lei, Jun Qiang, , , Alex Wong, , Qiong Shi &
Chinese mitten crab, Eriocheir sinensis, has been one of the most famous representatives of crustacean in China. Its transition from swimming type to crawling during the early development process, anadromous migration for growth, and catadromous migration for breeding have been attractive for research. However, the knowledge about the underlying molecular mechanisms to regulate these processes is still very limited. A total of 258.8-Gb raw reads for crab whole-genome sequencing were generated by the Illumina HiSeq2000...

Peer review of \"Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding\"

Taras K Oleksyk
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Sequence Compression Benchmark (SCB) database—A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences\"

Diogo Pratas
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Sequence Compression Benchmark (SCB) database—A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences\"

Diogo Pratas
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Imputing missing RNA-sequencing data from DNA methylation by using a transfer learning–based neural network\"

This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"A generalizable data-driven multicellular model of pancreatic ductal adenocarcinoma\"

Thomas Gorochowski
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"PhaseME: Automatic rapid assessment of phasing quality and phasing improvement\"

Cinta Peguerole
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"PhaseME: Automatic rapid assessment of phasing quality and phasing improvement\"

This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"EHRtemporalVariability: delineating temporal data-set shifts in electronic health records\"

Emre Guney
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Assessment of fecal DNA extraction protocols for metagenomic studies\"

This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Assessment of fecal DNA extraction protocols for metagenomic studies\"

This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Laniakea: an open solution to provide Galaxy “on-demand” instances over heterogeneous cloud infrastructures\"

Björn Grüning
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C\"

This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"ShinyLearner: A containerized benchmarking tool for machine-learning classification of tabular data\"

Stephen Eglen
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Multi-dimensional machine learning approaches for fruit shape phenotyping in strawberry\"

Mao Li
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"The gene-rich genome of the scallop Pecten maximus\"

Roger Huerlimann
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"The gene-rich genome of the scallop Pecten maximus\"

Takeshi Takeuchi
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Annotation and analysis of three crocodilian genomes

RE Green, EL Braun, J Armstrong, D Earl, N Nguyen, G Hickey, MW Vandewege, JA St John, S Capella-Gutiérrez, TA Castoe, C Kern, MK Fujita, JC Opazo, J Jurka, KK Kojima, J Caballero, RM Hubley, AF Smit, RN Platt, CA Lavoie, MP Ramakodi, , A Suh, Isberg, L Miles … & DA Ray
Crocodilians are important model organisms in fields as diverse as developmental biology, osmoregulation, cardiophysiology, paleoclimatology, sex determination, population genetics, paleobiogeography, and functional morphology. Crocodilians, birds, dinosaurs, and pterosaurs comprise a monophyletic group known as the archosaurs. Crocodilians and birds are the only extant members and thus crocodilians (alligators, caimans, crocodiles, and gharials) are the closest living relatives of all birds. To provide context for the diversifications of archosaurs, we generated draft genomes of three crocodilians,...

Supporting material for: \"Rapid detection of structural variation in a Human genome using nanochannel-based genome mapping technology\"

HZ Cao, AR Hastie, D Cao, ET Lam, Y Sun, H Huang, X Liu, L Lin, W Andrews, S Chan, S Huang, X Tong, M Requa, T Anantharaman, A Krogh, H Yang, H Cao & X Xu
The nanochannel-based Genome Mapping technology, commercialized as the Irys Platform, automatically images fluorescently labeled DNA molecules in a massively parallel nanochannel array. This technology has previously been used to map the 4.7-Mb highly variable human MHC region, as well as for de novo assembly of a 2.1-Mb region in the highly complex Aegilops tauschii genome, lending great promise for use in complete genome sequence analysis. Here, we apply this rapid and high-throughput genome mapping method...

Gene-set of brown planthopper genome

Wang Zhuo, Yu Li-Li, Zhou Xin & Zhang Chuan-Xi
The brown planthopper, Nilaparvata lugens, the most destructive pest of rice, is a typical monophagous herbivore that feeds exclusively on rice sap, which migrates over long distances. Outbreaks of it have re-occurred approximately every three years in Asia. It has also been used as a model system for ecological studies and for developing effective pest management. The N. lugens population sequenced in the present study was originally collected in Hangzhou, China, in 2008 and had...

Supporting materials for: \"VirAmp: A Galaxy-based viral genome assembly pipeline\".

Y Wan, DW Renner, I Albert & ML Szpara
We have developed a multi-step viral genome assembly pipeline named VirAmp, that combines existing tools and techniques and presents them to end users via a web-enabled Galaxy interface. Our pipeline allows users to assemble, analyze and interpret high coverage viral sequencing data with an ease and efficiency that was not possible previously. Our software makes a large number of genome assembly and related tools available to life scientists and automates the currently recommended best practices...

Supporting materials for \"BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ\"

Anthony Bretaudeau, Cyril Monjeaud, Yvan Le Bras, Fabrice Legeai & Olivier Collin
Many bioinformatics tools use reference data, such as genome assemblies or sequence databanks. The Galaxy web-based platform for data intensive biomedical research (http://usegalaxy.org/) offers multiple ways to give access to this data through its web interface. However, the process of adding new reference data was customarily manual and time consuming, even more so when this data needed to be indexed in a variety of formats (e.g. Blast, Bowtie, BWA, or 2bit). BioMAJ is a widely...

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